The company, which is growing faster than its Big Pharma rivals, posted revenue of $1.09 billion (677 million pounds), ahead of analysts' forecasts, and earnings per American depositary share (ADS) of $1.28, which fell slightly short.
Chief Executive Angus Russell said it was a strong quarter for the company, helped by sales of its hyperactivity medicines in the United States as children returned to school, and the group would meet analysts' profit forecasts.
During this year market expectations for Shire's 2011 earnings have risen steadily and believe we are on track to meet these revised expectations, he told reporters on Friday.
Analysts have raised their 2011 forecasts for earnings per ADS to $5.22 from $5.05 three months ago, according to a company-supplied consensus.
Profit in the third quarter was hit by a row with GlaxoSmithKline
Finance director Graham Hetherington said Shire had not recognised $50 million of royalties so far this year because of the dispute.
Shares in the group, which have risen by 28 percent since the start of the year, were 0.9 percent lower at 1,956 pence by 2:55 p.m..
Analysts at Morgan Stanley said the results demonstrated Shire's robust earnings power.
Despite significant R&D investment, and the ongoing dispute with GlaxoSmithKline regarding 3TC and Zeffix royalties, Shire is well on track to at least meet market expectations, they said.
Shire's rare diseases franchise has benefited from long-running manufacturing problems at U.S. biotech company Genzyme, bought earlier this year by Sanofi
Genzyme is still struggling to get supplies of Gaucher disease drug Cerezyme back on track, and said last month that supplies would be limited until January. Full production of its Fabry medicine Fabrazyme has also been delayed.
Patients have switched to Shire's Vpriv and Replagal medicines, giving the British company a leading position in a small but highly lucrative market.
Russell said the value of the drugs, which can cost hundreds of thousands of dollars per patient per year, was recognised by paying governments and insurers.
Our price cuts have sometimes been non-existent on those rare disease drugs, and have averaged something around the four to five percent range, he said. That's testament to the reality of very effective treatments for serious diseases.
The group has also been boosted by strong demand for drugs to treat hyperactivity in the United States, where prescription sales rose about 9 percent in the third quarter, according to analysts.
Sales of Shire's amphetamine-based attention deficit hyperactivity disorder (ADHD) drug Vyvanse rose 32 percent to $200 million.
The group wants to extend sales of the drug into European markets and new therapy areas such as depression, schizophrenia and binge eating.
It reported a successful Phase III ADHD trial of Vyvanse in Europe on October 21, paving the way for the drug to be filed for regulatory approval in the region by the end of the year, Russell said.
Analysts at JPMorgan Cazenove have said that Vyvanse could secure half of the European ADHD market, with peak European sales by 2020 of $450 million.
Analysts, on average, had expected Shire, which has grown its drugs portfolio through acquisition, to report revenue of $1.07 billion and earnings per ADS of $1.30, according to Thomson Reuters and company-supplied data.
(Editing by Ben Hirschler and David Cowell)